Congenital heart defects (CHDs) are the most common serious birth defect and a leading cause of infant mortality. Affected individuals who survive infancy require substantial medical care and experience lifelong morbidity and early mortality. Despite their prevalence and impact upon public health, the etiology of CHDs is poorly understood. This gap in understanding limits our ability to prevent CHDs, assess risk and predict outcome. Our long-term goal is to address this gap by defining the genetic basis of CTRDs and using this information to develop preventive measures and provide precise medical management based on genotype. As CHDs are a heterogeneous group of conditions, we have focused our studies on subsets of CHDs for which there is evidence of a shared genetic basis. The studies proposed in this application are focused on cases with conotruncal and pharyngeal arch anomalies (conotruncal and related defects, CTRDs) that comprise at least 36% of all CHDs and are a prominent feature of the 22q11.2 deletion syndrome (22q11DS). To address the gap in our understanding of the causes of CTRDs, we have conducted both SNP- and CNV-based genome wide association studies as part of our current P01. While our studies of individual variants have been largely negative, our analyses of genes and gene-sets provide new insights regarding the contribution of common and rare inherited genetic variants to CTRDs. Hence, our continued efforts to address this gap will focus on identification of gene-sets that influence the risk of CTRDs. Specifically, based on the results from our studies as well as recently published findings, we hypothesize that: (1) CTRDs are influenced by the full range of variability (rare to common; de novo and inherited) in relevant gene-sets; (2) the number of disease- related variants within these gene-sets varies directly with CTRD severity; and (3) gene-sets associated with CTRDs in non-syndromic individuals are also associated with CTRDs in individuals with the 22q11DS. To test our hypotheses, we propose studies that will: (1) define gene-sets that influence the risk of CTRDs via common inherited genetic variants across the genome, (2) define gene-sets that influence the risk of CTRDs via rare genetic variants across the exome, and (3) establish the genetic basis of the full clinical spectrum of CTRDs. These studies will use existing array (n= 1,105 trios and 406/2,967 cases/controls) and whole exome sequence data (n= 750 trios) from cases with severe CTRDs, as well as newly generated data for cases with mild CTRDs (isolated aortic arch anomalies, n=400). We will assess gene-sets derived from human disease loci, developmental biological networks and expression data in collaboration with Projects 1 and 3. A novel application of genetic risk scores will be used to identify the component genes and variants that drive the association between CTRDs and each gene-set. We anticipate that this work will reduce the gap in our understanding of CTRDs by providing an explicit set of genes associated with CTRD-risk by way of common and rare variants that define the genetic architecture for the full spectrum of these common birth defects.